Weitzman, M. D. | Search bioRxiv

bioRxiv2018

Recombination between co-infecting herpesviruses occurs where replication compartments coales

Homologous recombination (HR) is considered a major driving force of evolution since it generates and expands genetic diversity. Evidence of HR between co-infecting herpesvirus DNA genomes can be found frequently, both in vitro and in clinical isolates. Each herpes simplex virus type 1 (HSV-1) replication compartment (RC) derives from a single incoming genome and maintains a specific territory within the nucleus. This raises intriguing questions about where and when co-infecting viral genomes interact. To study the spatiotemporal requirements for inter-genomic recombination, we developed an assay with dual-color fluorescence in situ hybridization which enables detection of HR between different pairs of co-infecting HSV-1 genomes. Our results revealed that when viral RCs enlarge towards each other, there is detectable overlap between territories of genomes from each virus. Infection with paired viruses that allow visualization of HR correlates with increased overlap of RCs. Further, inhibition of RC movement reduces the rate of HR events among co-infecting viruses. Taken together, these findings suggest that inter-genomic HR events take place during replication of HSV-1 DNA and are mainly confined to the periphery of RCs when they coalesce. Our observations have implications on understanding the recombination restrictions of other DNA viruses and cellular DNA.

microbiology↗

bioRxiv2018

Genotypic and phenotypic diversity within the neonatal HSV-2 population

More than 14,000 neonates are infected with herpes simplex virus (HSV) annually. Approximately half display manifestations limited to the skin, eyes, or mouth (SEM disease). The rest develop invasive infections that spread to the central nervous system (CNS disease or encephalitis) or systemically (disseminated disease). Invasive HSV disease is associated with significant morbidity and mortality, but viral and host factors that predispose neonates to these forms are unknown. To define viral diversity within the infected neonatal population, we evaluated ten HSV-2 isolates from newborns with a range of clinical presentations. To assess viral fitness independent of host immune factors, we measured viral growth characteristics in cultured cells and found diverse in vitro phenotypes. Isolates from neonates with CNS disease were associated with larger plaque size and enhanced spread, with isolates from cerebrospinal fluid (CSF) exhibiting the most robust growth. We sequenced complete viral genomes of all ten neonatal viruses, providing new insights into HSV-2 genomic diversity in this clinical setting. We found extensive inter-host and intra-host genomic diversity throughout the viral genome, including amino acid differences in more than 90% of the viral proteome. The genes encoding glycoprotein G (gG, US4), gI (US7), gK (UL53), and viral proteins UL8, UL20, UL24, and US2 contained variants that were found in association with CNS isolates. Many of these viral proteins are known to contribute to cell spread and neurovirulence in mouse models of CNS disease. This study represents the first application of comparative pathogen genomics to neonatal HSV disease. ImportanceHerpes simplex virus (HSV) causes invasive disease in half of infected neonates, resulting in significant mortality and permanent cognitive morbidity. The factors that contribute to invasive disease are not understood. This study reveals diversity among HSV isolates from infected neonates, and makes the first associations between viral genetic variations and clinical disease manifestations. We found that viruses isolated from newborns with encephalitis show enhanced spread in culture. These viruses contain protein-coding variations not found in viruses causing non-invasive disease. Many of these variations are found in proteins known to impact neurovirulence and viral spread between cells. This work advances our understanding of HSV diversity in the neonatal population and how it may impact disease outcome.

microbiology↗